KI_Platy_analysis_OTUSummary
Symbiont alpha-diversity - Grouped by Species
First, we look at how many Symbiodinium types (OTUs) and clades are present in each coral species:
Plot OTU and clade diversity by species
## OTUs Clades
## Platygyra 40 4
## Favites 61 4
## png
## 2Sample sizes for different coral taxa
## [1] 146## NULL## [1] 116## NULL## png
## 2## png
## 2Barplot by Symbiodinium Clade - Platygyra and Favites pentagona 
Barplot by Symbiodinium Hit - Platygyra and Favites pentagona 
Symbiont alpha-diversity - Grouped by Sites (and SampleType)
Next, we look at the number of Symbiodinium types (OTUs) and clades in coral at each Kiritimati site:
OTU and Clade Diversity by Site
## OTUs Clades Dist Subclades
## site27 67 5 1 32
## site30 87 5 1 36
## site32 26 4 1 16
## site40 10 4 1 8
## site3 7 4 2 7
## site25 14 4 2 10
## site38 19 4 2 15
## site8 47 5 3 24
## site14 10 2 3 7
## site34 56 5 3 29
## site35 86 5 3 30
## site5 23 4 5 13
## site37 7 3 5 5
## site15 31 4 6 18
## site19 5 2 6 5
## OTUs Clades Dist Subclades
## site27 13 3 1 9
## site30 6 3 1 5
## site32 14 3 1 9
## site40 6 3 1 5
## site3 7 4 2 7
## site25 11 3 2 8
## site38 3 3 2 3
## site8 6 3 3 5
## site14 6 2 3 5
## site34 15 5 3 11
## site35 11 4 3 9
## site5 14 3 5 9
## site37 6 3 5 5
## site15 7 3 6 7
## OTUs Clades Dist Subclades
## site27 13 4 1 11
## site30 11 3 1 7
## site32 14 3 1 11
## site40 6 3 1 5
## site3 2 2 2 2
## site25 5 3 2 4
## site38 10 2 2 7
## site8 5 2 3 5
## site14 6 2 3 5
## site34 14 4 3 10
## site35 5 2 3 3
## site5 10 3 5 8
## site37 4 3 5 3
## site15 27 4 6 15
## site19 5 2 6 5
OTU and Clade Diversity by Disturbance Level
Symbiont alpha-diversity - Grouped by Field Season
To understand how Symbiodinium diversity changes among field seasons, clade diversity is divided by field season. This includes coral-associated Symbiodinium.
OTU and Clade Diversity by Field Season
## OTUs Clades
## KI2014 27 4
## KI2015a 18 3
## KI2015b 33 4
## KI2015c 46 4
## KI2016a 21 4
Plot unique Symbiont types by coral taxa
## [1] 18## [1] 13## [1] 13## [1] 26## [1] 14## [1] 19
Principal and Background Types
Background Symbiodinium types are those which have <0.01% abundance, and Principal Symbiodinium types are those which ahve >0.01% abunance (per Quigley et al 2017).
Abundance vs. Prevalence
Rank Abundance Curves - all timepoints
Rank Abundance Curves - before and after (alive/dead corals only)
##
## Attaching package: 'reshape'## The following object is masked from 'package:dplyr':
##
## rename## The following object is masked from 'package:data.table':
##
## melt## Using Abundance as value column. Use the value argument to cast to override this choice
## Using Abundance as value column. Use the value argument to cast to override this choice## Warning in plot.histogram(r, freq = freq1, col = col, border = border,
## angle = angle, : the AREAS in the plot are wrong -- rather use 'freq =
## FALSE'
## [1] 5## [1] 18## [1] 0## [1] 5data.frame(sample_data(phy97.f.c.p))[which(data.frame(sample_data(phy97.f.c.p))$coral_tag=="594"),]## coral_tag SampleType field_season Coral_Species site Status
## KI15cFSYM114 594 coral KI2015c Platygyra_sp 15 alive
## KI15aFSYM043 594 coral KI2015a Platygyra_sp 15 alive
## KI16aFSYM158 594 coral KI2016a Platygyra_sp 15 alive
## ref Year_Pre_Post colony_width1 colony_width2
## KI15cFSYM114 2015July.tag594 NA NA NA
## KI15aFSYM043 2015Jan_Pre.tag594 NA NA NA
## KI16aFSYM158 2016March.tag594 NA NA NA
## colony_area binary_tissue_loss binary_disease
## KI15cFSYM114 NA NA NA
## KI15aFSYM043 NA NA NA
## KI16aFSYM158 NA NA NA
## cyanobacteria_contact binary_algal_contact turf_contact
## KI15cFSYM114 NA NA NA
## KI15aFSYM043 NA NA NA
## KI16aFSYM158 NA NA NA
## binary_macroalgae_contact type_of_macroalgae
## KI15cFSYM114 NA NA
## KI15aFSYM043 NA NA
## KI16aFSYM158 NA NA
## binary_CCA_contact sediment_contact binary_coral_contact
## KI15cFSYM114 NA NA NA
## KI15aFSYM043 NA NA NA
## KI16aFSYM158 NA NA NA
## binary_bleaching bleaching_proportion notes_bleaching Dist
## KI15cFSYM114 NA NA NA VeryLow
## KI15aFSYM043 NA NA NA VeryLow
## KI16aFSYM158 NA NA NA VeryLowplot_bar(phy97.f.c.p)
coral594 <- subset_samples(phy97.f.c.p,coral_tag=="594",prune=TRUE)
coral594 <- prune_taxa(taxa_sums(coral594) > 0.01, coral594)
plot_bar(coral594,fill = "hit")